A New Era
by Zenny01
Summary: THE LONG AWAITED SEQUEL TO SAFE HOUSE. The Sokovia Accords are over. But not everything is back to normal.
1. Chapter 1

_**Disclaimer: None of these characters are mine. Because if they were, Tony and Natasha wouldn't have died. Thanks!**_

**Hey everyone! I have gotten a lot of people asking for a sequel to Safe House and I finally got my life in somewhat of a state where I could begin writing this. I am so excited to begin writing this. The last two stories of this series were so much fun to write and I'm glad to be back with this story. Thank you for all of the support and love for Safe House. You guys are so amazing, and I am glad that I can make people happy with my writing. With all that said... let's get this show on the road! Please let me know what you think and don't forget to follow and review this story!** _**PLEASE NOTE: THIS IS THE THIRD PART OF A SERIES. I WOULD RECCOMEND YOU READ THE OTHER PARTS FIRST. THANKS!**_

**SUMMARY: **THE LONG AWAITED SEQUEL TO SAFE HOUSE. The Sokovia Accords are over. But not everything is back to normal.

_**Also last warning... if you haven't read the first two works of this series, please do! It may be a bit difficult to follow this story if you haven't read the last one.**_

/./_THISISALINEBREAK_/./

A scream tore out of Peter's throat as he shot up in bed. His breaths were heavy and quick as if he was afraid all of the oxygen would be stolen away at any given moment. Sweat dripped down his skin wetting the silk sheets of his bed. He had been there again, being cut open and dissected like a lab rat. The image of that cursed place was ingrained in his memory and he couldn't get it out. This wasn't the first time he'd woken up like this. Ever since he'd been rescued from the Raft prison, he'd been having nightmares. He was afraid to sleep because every time he did he was visited by visions of that hell.

"Peter!" a voice called out from the hallway. He didn't respond. Even if he wanted to, he didn't think he could. He was still hyperventilating, the room still felt like it was closing in on him. The familiar ring of his spider-sense beat in the base of his skull. What if this wasn't real? What if the last few months had only been a hallucination? A horrible side-effect from the drugs they were constantly giving him. God, he was still there, wasn't he? None of this was real it was all fake. They never came for him… why would they?

Any moment now he'd wake up from this dream and be faced with reality. Ross would be standing outside of his 6x8 cell with that sickening smirk on his face, a needle in his vile hand. Chains would be around his wrists and he would try to see around the completely dark cell only to step in his own waste. There would be no noise at all and he would desperate for any kind of sound. Anything to let him know he was still alive.

He suddenly felt like he was suffocating. His hands flew to his throat as he could feel the chaffing of the collar around his neck. The collar that made him as obedient as a dog, that kept him caged in this inferno. He had to get it off. He tore at his skin trying to rip it away from his flesh. He pulled and pulled and pulled but it wouldn't move. He could feel a cool liquid coating his fingers as he clawed at the device desperately. Sobs wracked his emaciated frame as the feeling of the collar squeezing around his neck refused to leave.

Hands grabbed his wrists, tightening slightly. Peter flinched away at the touch trying to get away from whoever was touching him.

"Peter! Peter calm down it's me. It's just me, open your eyes. You're safe."

That sounded like Tony. But that wasn't possible, he was on the Raft, wasn't he? Strong arms engulfed him in a hug as he continued to lose himself in the confusion of what was real and what wasn't. He didn't know anymore. Right now, all he cared about was the feeling of warmth that the embrace provided him with. If someone was holding him, if someone was talking to him, then he couldn't be dead. That was enough.

Someone's fingers carded their way through his hair as the long wails and sobs turned into short whimpers and whines. The banging of his spider-sense reduced to a dull throb allowing him a moment of relief. He still didn't remember where he was, but he didn't care. Exhaustion quickly overtook his body, his eyes beginning to droop close against his wishes. He didn't want to go to sleep, he didn't know what he'd wake up to.

"Shh. You're ok, Peter. I'm not going to let anything happen to you."

For some reason, he trusted that voice. It was ok. It would be ok. Wouldn't it? It didn't matter. He couldn't stay awake any longer. Darkness began to flood his vision, a brief moment of panic overcame him at the lack of light, but he was soon too unconscious to care.

Tony sighed as Peter finally sagged in his arms. He didn't know what he'd been thinking. What the hell was he doing? He didn't know how to raise a kid let alone one who had been traumatized like Peter. He looked down at the boys sleeping form sadly. This was his kid now, he would do everything in his power to help him, but this was out of his control. That was a terrifying thought.

He always preferred to be the one in control. If he was in control, then no one would ever have to go through what he did when he was kidnapped. But in an effort to gain control, he lost it to a power-hungry general who did exactly the opposite of what Tony wanted. He hunted Spider-Man like a damn criminal, killed Peter's aunt, forced him to go on the run and leave his whole life behind, and then kidnapped and tortured him. This was his fault. He'd let this happen. Peter was in this situation because of him.

Sighing, Tony lay Peter down on his bed separating his hands were they clenched tightly to his now soaked shirt. He stood up glancing at the boy before silently making his way out of the room. He closed the door trying not to wake the sleeping teen. A short breath of relief escaped past his lips when he let go of the door handle.

"How is he?"

Tony nearly jumped when he heard the voice. Turning around he saw the familiar face of his… teammate? Were they a team again? After everything that had happened with the Sokovia accords falling apart, Ross' arrest and subsequent admittance into a mental hospital thanks to whatever Wanda did to him on the Raft, and Peter coming home for the first time in months, the group never talked about what came next. Everyone was staying at the tower at the moment, but everything was far from normal.

"Stark," Natasha prompted when Tony didn't immediately respond, "Is Peter ok?"

Tony shook his head as he looked over the former spy. She was wearing a black tank top and blue leggings that cut off slightly above her ankles. Her hair had grown longer, returning to its natural shade of red with parts of platinum blonde still weaved in. At the moment it was up in a messy bun, small waves of it framing her face below.

"No, he's not."

Natasha looked down sadly. She knew what happened to Peter on the Raft. Ross' brain may have been in ruins, but most of the guards who remained alive were not so lucky. When she couldn't get information the conventional way, she got it unconventionally. She was horrified by what she found. Experiments, dissections, drug tests, endurance tests. It was all terrifyingly familiar, but Peter didn't deserve that kind of stuff. She looked past Tony to the door of the kid's room wishing desperately she could change everything.

"I'll be in my lab," Tony said when she didn't respond. He quickly turned and left not wanting to face the awkward situation.

Natasha watched as he stalked away before turning and heading back to her own room. She walked around the floor a couple of times before going in, paranoia from her days as a fugitive still at the surface of her mind. She made her way through the dark room stealthily before reaching the bed. She climbed in her mind still racing with thoughts about Peter.

The bed shifted as the figure next to her moved. Strong arms wrapped around her petite frame as she sighed.

"What happened?" Steve asked quietly from beside her.

"He had another nightmare," Natasha responded not needing to clarify who it was. "Tony was already there."

Steve nodded pensively as she snuggled into his chest.

"Are you ok?"

"I'm fine," Natasha lied. "Go back to sleep."

"You sure?"

"Go to sleep Steve," Natasha repeated memories of Russia playing over in her head. She couldn't shake the feeling of dread that was overtaking her. Ross may have been defeated and the Sokovia accords may have been scrapped. But this new era that was beginning, didn't seem to be any better than the last.

**AUTHOR'S NOTE: ****So... what'd you think? I thought long and hard about where I wanted to take these characters and I feel like this is the best option I came up with. I am really interested to know what your opinion is though. Please write a review to let me know. Thanks!**** Until next time!**


	2. Chapter 2

**DISCLAIMER: I DO NOT OWN MARVEL OR ANY OF IT'S CHARACTERS.**

**Hey guys! I finally got my act together enough to get the next chapter up. Please let me know what you think. R&R! Enjoy!**

The faint glow of sunrise illuminated the dark room as Peter tossed and turned in bed. He'd woken up again earlier that night, and since then sleep had evaded him. It wasn't for lack of trying. But every time his eyes began to droop, heavy with sleep, he would be jolted awake. Sometimes it was by a memory of the Raft. He could feel the operating table underneath him as a knife ripped him open for dissection. Or he'd experience a phantom needle penetrating his skin forcing his systems to flood with adrenaline. The imagined shock from the collar wrapped around his neck caused him to shoot up from the bed multiple times.

Other times it wasn't a memory that interrupted his rest, but simply a feeling. The overwhelming sense of dread would wash over him leaving him with a horrible pain. He wouldn't be able to see anything, but that sense of trepidation was more than enough to arouse him from his slumber. The worst part was that the feeling never went away. It got better, more manageable during the day. But it was always there, tickling the back of him mind and worming its way into his life.

A knock at the door caused him to jump, flinching backwards as the sound echoed across the barren room. Falling off the bed, he nearly screamed in fright, but caught the cry before it was unleashed. Everyone was already worried enough. Screaming would only increase their concerns.

"Peter!" Steve called through the closed door. Peter only stared at the door. He wanted to move, to call out to the first avenger and tell him he was all right, but he couldn't. His feet were planted firmly on the ground seemingly glued in place. He opened his mouth to respond but no sound came out. It made no sense to him. A moment ago he was fighting to keep himself from speaking, struggling to keep it all in. And here he was with someone to talk to, but he couldn't. There was no logical explanation for it, but his voice was trapped inside his own body.

"I know you're awake," Steve said from outside. Slowly Peter made his way to the door. He put one foot in front of the other hesitantly, as if asking permission before taking any step. Inching his way forward, he stopped in front of the door. There was that feeling again. That one that kept him awake at night and haunted his every action during the day. His heart was beating quickly, thumping at the speed of a locomotive. He licked his lips trying to stop his entire mouth from going dry.

A hand reached for the door handle. He knew it had to be his own, but he couldn't feel it. He watched it closely, feeling completely detached from himself. The cool metal of the doorknob connected with his skin, but he still felt nothing. It was as if he was observing everything from another perspective. He knew he'd opened the door, and he knew he'd talked to Steve, but he didn't remember it. The entire experience seemed so fake. Maybe this wasn't really real.

A hand suddenly pushed down on his shoulder startling Peter. Instinctively, he shoved the person back panting heavily as he threw the hand off of him. Something was wrong, he was in the kitchen. When did he get there? He hadn't been there before. He was in his room, and then… what happened after that? He didn't remember anything. Why couldn't he remember anything!?

"Peter it's ok! It's just me!"

He looked up to find Steve staring at him with a concerned expression on his face. Its ok. He knew who Steve was. Peter took a deep shuddering breath and closed his eyes trying to convince his spidey sense that there was no danger. The ringing at the base of his skull had increased tenfold and it was making it difficult to focus on everything.

"Are you ok?"

Was he ok? No not really, but he couldn't burden the older man with that. He was already checking up on him every couple of hours. If Steve knew what was really going on inside of his head he'd never leave. Sometimes the presence of the other avengers could be suffocating. They coddled him like a newborn, dancing around heavier topics or simply not discussing them. He was grateful they cared so much, but it was a bit overwhelming.

"Yeah," Peter breathed out a few octaves higher than he would've liked. He glanced in the direction of the super soldier scrutinizing him. The man's eyes narrowed slightly, but he seemed to let it go for the moment.

"If you ever need anyone to talk to," Steve began calmly.

"I know who to come to."

Steve nodded before grabbing the plates that were set on the island in front of them. Dropping them in the sink to wash he watched Peter out of the corner of his eye.

"I think MJ is coming over today," he prompted, hoping to get a response from the spiderling.

Peter looked up at that. He really missed MJ. He hadn't seen her since he'd gotten rescued from… since he'd gotten rescued. It wasn't because he didn't want to, but after he was cleared from the hospital and moved into the tower with the team, he didn't really do much of anything.

"That's good," Peter responded with more energy in his voice then there had been in a long while. "I really miss her."

"Well it's a good thing I invited her," Natasha chimed in as she walked into the room. Walking next to Steve, she reached up and grabbed a coffee mug from the cabinet. "She seemed excited."

"You invited her?" Peter asked.

"Yeah," Natasha replied nonchalantly. She set the coffee cup under the machine to brew and within seconds, the bitter-sweet aroma of espresso flooded the room. "Why do you ask?"

"You're her favorite avenger. She's always wanted to meet you."

"I guess she's going to get her wish."

Peter smiled. Outwardly, Natasha did not show any emotion. But on the inside she was elated and relieved. It had been months since Peter had smiled or even really carried a conversation like this. It was progress. More than there had been in far too long.

"You might want to change," Steve said turning the water off as he finished the dishes. "She arrives in less than an hour."

Peter looked down at his Star Wars pajamas and nodded. He walked out of the room quickly moving with an energy that had been dormant for eons.

"You know there's a machine that washes the dishes for you right?" Natasha asked playfully.

"Do you think Peter is going to be ok?"

Natasha sighed.

"Honestly I don't know," she replied softly. She grabbed her coffee and leaned on the countertop next to Steve.

"I wish I could help more. I know what he's feeling, what he's going through. I still feel that sometimes."

"I know. I do too."

They sat there for a while in a comfortable silence simply enjoying each other's company. Eventually, the black elixir was drained from the mug and Natasha turned to set it down on the counter. The feeling of uneasiness had settled a bit since the night before but something was still off. Something was wrong.

"I ummm…" she stumbled over her words slightly, cursing at herself for doing it. "I'll be back." She forced out finally. "I need to take care of something."

"Ok, I'm going to head down to the gym for a bit," Steve said pushing off the counter. She knew what that meant. Even though he'd never admit it, this thing with Peter was really bothering him. He went to the gym to work out frustration or memories. It was his coping mechanism. It had been since the day they met. She desperately wanted to change that. To be there for him in a better way than a punching bag ever could, but she couldn't. Not right now.

"Sounds good," She replied instead tilting her head up to place a kiss on his lips. "I'll catch up with you."

Turning around she made her way out of the kitchen dragging herself back upstairs to their shared bedroom. Making her way inside she flopped on the bed in frustration. Inhaling slightly when a jagged object pushed on her stomach. Her heart nearly stopped. Carefully, she removed herself from the covers swooping off the sheets to reveal a small white letter. Picking it up, she inspected the envelope turning it over. Her name was written on the front. _Natalia__. _The handwriting was in neat cursive, but she couldn't tell much else.

She sat down before using her shaking hands to pry open the letter.

_Natalia Alianovna Romanoff,_

_You have forgotten what you are, and what you serve. Your treachery has gone unpunished, some even hoped you'd repent. But I always knew you better than that, Natalia. You are a traitor to the red room. To your people. You must pay for your crimes. I am coming for you, Chernaya Vdova. And when I am done, you will watch your world burn to ash._

_Madame B._

**Author's Note:** **What'd you guys think? I am going to be focusing mainly on Natasha and Peter for this story as I feel these to characters have a lot of room to grow. Please review this story. The more reviews, the more motivated I am to write the next chapter.**

**PS. Did you guys see the Black Widow trailer!? If not, you're missing out. It looks so damn good. My hype levels are through the roof.**


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